django-phenotype-ontologies 0.2.6

Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)

=============================
Django Phenotype Ontologies
=============================

.. image:: https://badge.fury.io/py/django-phenotype-ontologies.svg
:target: https://badge.fury.io/py/django-phenotype-ontologies

.. image:: https://travis-ci.org/chopdgd/django-phenotype-ontologies.svg?branch=develop
:target: https://travis-ci.org/chopdgd/django-phenotype-ontologies

.. image:: https://codecov.io/gh/chopdgd/django-phenotype-ontologies/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/chopdgd/django-phenotype-ontologies

.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Updates

.. image:: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/python-3-shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-phenotype-ontologies/
:alt: Python 3

Django app to parse/load phenotype ontologies (OncoTree, HPO, MONDO, etc)

Documentation
-------------

The full documentation is at https://django-phenotype-ontologies.readthedocs.io.

Quickstart
----------

Install Django Phenotype Ontologies::

pip install django-phenotype-ontologies

Add it to your `INSTALLED_APPS`:

.. code-block:: python

INSTALLED_APPS = (
...
'phenotype_ontologies',
...
)

Add Django Phenotype Ontologies's URL patterns:

.. code-block:: python

from phenotype_ontologies import urls as phenotype_ontologies_urls


urlpatterns = [
...
url(r'^', include(phenotype_ontologies_urls, namespace='phenotype_ontologies')),
...
]

Features
--------

* syncs OBO from MONDO, HPO, and NCIT (OncoTree)
* REST API to interact with models
* GraphQL Nodes to be incorporated to existing GraphQL setups with graphene_django

Running Tests
-------------

Does the code actually work?

::

source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ tox

Credits
-------

Tools used in rendering this package:

* Cookiecutter_
* `cookiecutter-djangopackage`_

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage




History
-------

0.1.0 (2018-04-10)
++++++++++++++++++

* Models for Phenotype Ontologies
* REST API
* GraphQL Nodes
* Sync methods for PURL of MONDO, HPO, NCIT

0.1.1 (2018-04-10)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.0...v0.1.1>`_

* Updated sync to sync_ontology to make it more descriptive

0.1.2 (2018-04-10)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.1...v0.1.2>`_

* Added better support for MONDO. A few oddities were causing errors w/ pronto.

0.1.3 (2018-04-18)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.2...v0.1.3>`_

* Updated 3rd party libs

0.1.4 (2018-05-16)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.3...v0.1.4>`_

* Updated setup.py to read from requirements.txt


0.2.0 (2018-06-01)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.1.4...v0.2.0>`_

* Removed support for GraphQL

0.2.1 (2018-07-27)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.0...v0.2.1>`_

* Updated NCIT to be OncoTree - since we are using the onco tree specific ontology

0.2.2 (2018-08-13)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.1...v0.2.2>`_

* Updated 3rd party requirements. Some requirements had changed so it was causing failures

0.2.3 (2018-10-29)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.2...v0.2.3>`_

* Updated 3rd party requirements.

0.2.4 (2018-11-27)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.3...v0.2.4>`_

* Updated 3rd party requirements.

0.2.5 (2019-02-08)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.4...v0.2.5>`_

* Updated 3rd party requirements.
* Updated tests to use py.test fixtures

0.2.6 (2019-04-10)
++++++++++++++++++

`Full Changelog <https://github.com/chopdgd/django-phenotype-ontologies/compare/v0.2.5...v0.2.6>`_

* Updated 3rd party requirements.
* Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3